Healing Wounds
by theyhadadate
Summary: The Doctor's regenerated yet again, except this time he has more to deal with, including a triple crossing agent, Torchwood, cases, and Miracle Day. AU
1. Chapter 1

_**Okay, smack me with a stick- and blame Tumblr as well! This is fairly dark, like... double death in first chapter and don't even start- I cried writing it. But that's what my muse is coming up with, my loves.**_

_**Disclaimer: Not a thing, dearies.**_

_****Yo'iolyr, 3094_

It's a piercing scream that breaks the standoff between the man in the bow tie and tweed and the devilish looking creature hissing at him, the wail echoing around the caverns. It draws the bow tie man's attention, the split second of worry giving the beast a moment to lunge, sending both into a tumble of limbs and fur and hair on the floor. Another cry ripped through the scuffle, the man finally pushing the monster off of him and running down one of the many tunnels open to him, following the sound of screams and yells.

The man burst into the next room, waving something like a torch in front of him, looking at it as if he could glean some type of reassurance from the device. A frown, instead, appeared, and the man dashed down an adjoining tunnel, moving the torch-like instrument in front of him back and forth, checking it periodically. Another scream pierced his ears, spurring him on as he burst into a large domed cavern, dread filling him as he looked on.

Dozens of the beasts were swarming around two figures near the center of the room, one a long haired ginger, another wielding a broom or mop of some sort. The ginger had her mouth primed for another call before her eyes fell on the man who had entered the room. Her eyes lit up for a second. He had come back for them after all; she knew he'd never leave her behind. The man took a step towards the two people who had been there with him for so much, already reaching for the two of them.

The smile rapidly disappeared from the ginger's face as a creature grabbed her, wrenching her farther away from her two men. Rage showed on the faces of the two men, one using his mop to beat the creatures out of the way, and other pushing and shoving. Another scream pierced the air, scattering the monsters back into the tunnels. A gruesome sight awaited the two.

Her ginger hair was splayed about, a shiny red fan of locks framing a deathly pale face. And the blood, the slowly growing pool of blood stemming from wounds in her back and on her sides. She was gasping for breath, alternating between two names, eyes searching blindly for somebody."Rory," she whispered faintly. "Doctor."

The man in the bow tie backed away a bit, giving the other man and his wife some space. "I'm right here, Amy," Rory said softly. "Just hang on a moment, we're gonna get you out of here and you're going to be okay." His voice broke at the end, sliding his hand into hers. It was icy compared to his skin. "Please, Amy."

A sad smile flickered weakly across her face as she shook her head slightly. "Not this time, Rory," she croaked, squeezing his hand with what little strength she had. Her head turned slightly. "Doctor," she called.

The Doctor moved to her other side quickly, taking her hand in both of his. "Oh, Amy Pond… Glorious, brilliant Amy Pond… I never meant for this to happen." He took in the way she looked, red hair surrounding a pale face like a fiery halo, red hoodie half ripped to shreds, a pool of blood under her. "I am so sorry, Pond…"

"Shut up." And for a moment, she sounded alive again, like she had so many times in their travels. The Doctor and the Ponds in the TARDIS, off to cause some havoc somewhere in time and space. Then she coughed, wheezing, and it was lost. "Doctor. My Raggedy Doctor. My best friend. Promise."

"Anything, Pond."

"Keep Rory safe…" Amy's voice cracked. "Keep him safe." Her eyes flickered over to where her husband kneeled by her side. "Rory…"

"Amy, please…"

"I love you, you silly face." Amy smiled at him weakly. "Now hush, both of you."

Silence fell on the three, Amy's hands encased in Rory and the Doctor's. Her eyes were glued to Rory's the entire time. Her eyes fluttered again, and her hands went limp. Rory ducked his head, tears brimming in his eyes, pressing his wife's hand to his lips over and over. The Doctor bent over Amy, planting a kiss on her forehead for the last time, and laid her hand over her stomach. Standing up, he moved up and away, pointing the torch-like instrument at nothing in particular. A deep whooshing noise filled the room, a light wind ruffling through as a blue police box materialized where he had been pointing it.

"Rory." The Doctor turned once more to face his grieving companion. "Rory, we need to go before the others return." The nurse didn't move, still holding his wife's hand to his lips. "Rory, I know it hurts but we need to go!"

"She's gone." Rory's voice was quiet. "She can't be gone."

"Rory, I am so sorry…" The Doctor was stricken. "Help me move her back to the-"

He was cut off as the beasts returned, roars echoing around him and rebounding off the walls. Rory placed his wife's hand down next to her, grabbing his mop off the floor and brandishing it like a sword. The monsters swarmed around them, the two men on either side of Amy's body, trying to save themselves and her. "Doctor, just go!"

"I promised Amy I'd keep you safe!"

"Just get out of here, Doctor." Rory turned his head slightly to give the Doctor a stern look. "We won't be able to get her out of here and still be alive. And I won't leave her." He turned back to the creatures, kicking one sharply in the abdomen. "GO!"

The Doctor hesitated before dashing through a small break in the creatures. Fumbling with a key, he unlocked the door and pushed it open, sending a tortured look to Rory before darting inside. The whooshing noise filled the room again, the box dematerializing and leaving.

Rory closed his eyes for a moment, listening to the comforting vworping of the TARDIS. The Doctor, the TARDIS, all of time and space, Amy… he'd seen it all, he'd lived the life of a time traveler. He saluted briefly at the disappearing box, smiling faintly as he returned to the futile task at hand. He'd gotten the Raggedy Doctor out, and he was going to be with his Amy forever; his beloved, brilliant, beautiful Amelia Jessica Pond.

She was the last thing he saw before he felt the sharp thud on the back of his head and everything went dark.

_**I will be in the corner with a bucket for my creys.**_

_**Next chapter: The Doctor reflects on the Ponds' passing, and encounters a fairly strange woman...**_


	2. Chapter 2

_**WHOOO. School got canceled because of the wind and power outages! YAY!**_

_**I'm working on this as best I can, but I'm liking the way it's turning out.**_

_**Disclaimer: Not mine!**_

_Time Vortex_

The Doctor leaned against the console, staring blankly into space. It was as if someone had punched a hole into his chest and pulled out both of his hearts. Amy Pond. Rory Williams. Two of the most wonderful people he'd ever met in his travels, both dead because of him. He could remember the first time he met Amelia Pond; she had been so very young, she believed in him with all her heart. Amy Pond, the girl who waited for him to come back and sweep her away in the blue box that was bigger on the inside and went everywhere in time and space.

Rory Williams. The Last Centurion, the voice of reason on the TARDIS when Amy and the Doctor got carried away. He waited too, he suffered because of the Doctor; he'd died several times, he'd been plastic. He'd paid the price for being a friend of the Doctor with his wife.

It wasn't right. It was always the best of the best that ended up dying or suffering for him in the end. He had watched secretive River Song sacrifice herself in his place in the Library. He had held brilliant Donna Noble after wiping her mind of all traces of him and their travels. He'd leaned against that wall that separated him from his Rose Tyler when she had been trapped, thought to be lost forever. He had held his wonderful Jenny after she'd taken a bullet for him. And it wasn't fair.

He was the man who had kept on running; the man who left. He'd run this time because Rory had told him to, and Rory would've physically shoved him away if he'd stayed. He hadn't wanted to run.

But he did.

-o-o-o-

_Cardiff, December 2013_

Heels clicked quickly on the cement, moving purposefully and smoothly as they flitted away. The shoes gleamed slightly in the light from the buildings and the lamps, the shiny black material blending into the night. The owner of the shoes was well dressed; the form fitting royal blue dress clung to her curves, a cloud of taffeta swirling from her waist to her knees. A short black sweater protected her from the cold chill of the night. A small blue bag was held at her side. Her caramel waves were swept up into a simple French twist, a few tendrils framing her face. Brown eyes scanned the night, searching curiously.

"I didn't expect to see you wandering around so late, Miss Adler." A man pushed himself out of an alley and fell into step with her, his long blue coat billowing behind him in the slight breeze. "You really shouldn't be allowed to dress like that and walk alone." He stopped her and offered his arm, giving her a smile that made most people forget exactly what they were saying.

It didn't work on her. "I can take care of myself, Captain, you surely know that." Though her tone was cold, the faint smile she offered him was warm. Looping her arm through his, she pulled him along gently. "But I thank you for your concern. What are you doing out so late? I thought you'd still be at the Hub."

"Ah. Well. Gwen is taking care of it. It's been coming along nicely, rebuilding the place after…" He trailed off, looking down. "It's nice, having Rex there too. But, God, it's not the same." A soft sigh escaped him. "You've been a real help, though, Irene, really." He grinned at her again. "You're a real asset to the team."

"Thanks, Jack. I wonder if _he'd_ be at all proud of what I'm doing. I never told _him_." The way she pronounced the pronoun made it sound as if this unknown man was anything but normal, that he was important.

"You really think he's going to come back, don't you?" There was a bitter tone to Jack's voice as they walked. "He's not the type to look back, I would know. Stay on with us here, there's nothing left in London."

Irene's eyes glazed over for a moment. "Maybe," she whispered.

Jack smiled at her, patting her hand. "Let me know. Wanna go get a bite?"

"That sounds nice."

"And really, what were you doing out so late?"

A ghost of a smile flickered over her lips. "As I was told."

-o-o-o-

_Luna, March 5152_

The Doctor staggered through the streets, one foot falling in front of the other as he tried to find his TARDIS. One hand was clutched to his stomach, where a ghastly looking wound was slowly sapping what little strength the Time Lord had left. He'd dived in front of an energy blast to protect a friend. He knew what would happen next, he remembered. The golden light would engulf him, and quicker than he knew it he'd have a new face, a new voice…. Just all… new.

The bright nightlife of the 52nd century lit his way to the dirty alley in which his TARDIS was parked. The TARDIS, the one companion who would always be there for him.

_It's always just you and her, isn't it, Doctor? A mad man and his blue box, off to see the universe. Always the two of you, when us companions are gone._

He hadn't taken on another companion after the Ponds. He couldn't. He wouldn't risk putting them through what they had gone through at the end, a gruesome death. The Doctor cared.

The Time Lord leaned on the box, his hands moving to unlock the door, staggering in and nearly falling on his face as he closed the door. The TARDIS was humming- welcoming him home, trying to soothe him. It took a great deal of energy to climb up to the console, and he panted, using it as a support. "One more trip, old girl, for old times' sake?"

With difficulty, he wrenched himself up, flicking the controls on the console once more and dematerializing the TARDIS. As he did so, he noticed it. A shimmering flicker of color.

The golden glow around his hands slowly engulfed him as the TARDIS disappeared.

-o-o-o-

_Cardiff, December 2013_

"As you were told," Jack mused over a cup of coffee, glancing at his friend. "That's not very…"

"Informative? I know." Irene snickered, taking a sip of her hot chocolate. "Trust me, you really don't want to know. It's all… fairly confusing, even for me." She reached into her bag and pulled out a small, dark blue envelope. Not noticing how Jack's eyes widened as they recognized the color, she continued. "He gave it to me, fairly soon after we'd met in London. Said that one day, it'd be important. Also said I wasn't allowed to open it unless it made sense to. Plus, he said to be in Cardiff today, so here I am."

Jack cleared his throat. The envelope was the perfect shade of TARDIS blue. But it was only a coincidence, right? Wrong, he thought. The Doctor had taught him that. "Well, doesn't it make sense to open it now?"

"I guess so." Sliding her finger carefully under the flap, she ripped the top, pulling out the contents of the envelope. A piece of paper, folded up small, and a shiny silver key. A frown creased her forehead as she unfolded the paper, looking it over.

Jack watched her carefully, reaching for the key and examining it. There was no doubt about it; it was a TARDIS key. But why would've Irene's friend- lover- whatever the hell he was give her one? His eyes fell on her as she tucked the paper back in the envelope and slid it back in her bag, sighing. "What was that?"

"A letter." Her tone made it evidently clear she didn't wish to discuss further. Jack huffed, pushing forward anyways.

"And what did it say?"

"That, Jack, is absolutely none of your business." She stood abruptly and took the key from him, sliding it in her bag. "I have to go."

"Wait, what?"

"I'll meet you at the Hub in the morning before I catch my ride back to London. It's good having me out there, isn't it? Two years of me keeping an eye out for the little ticks you're oh so fond of, Captain. While you take care of the Rift, I keep an eye out when we get attacked, since London seems to get attacked fairly often." Irene swooped down to peck his cheek before turning sharply and moving away, heels clacking as she walked.

Jack stared after her, amused. She was a hell of an asset to Torchwood.

-o-o-o-

The Doctor patted himself, feeling his face, checking to make sure he had all his fingers and eyes and nose and such. Disappointed to find himself yet again, not ginger, he left the Console room to change into something a tad bit warmer. By the readings he'd seen, he'd landed in Cardiff, sometime in December 2013.

It definitely called for a change of clothes. He made his way to the wardrobe, passing a mirror as he entered. It stopped him, his reflection. Black hair, pale, blue-gray eyes. It was different. But he liked it, although the tweed just didn't do with this outfit. Something a little more… sophisticated, perhaps.

A loud growl caught his attention. "Oh, I'm hungry!" He blinked at the sound of his voice. "New voice. That's different."

-o-o-o-

Irene sat in the stuffy café, muttering to herself. Why would Sherlock have told her to go here? It didn't really make any sense, and that was coming from her. With a huff, she pulled out the letter again and looked it over.

_Irene (For a short moment there, I contemplated something sappy, then I thought better of it),_

_It is of the utmost importance that you do exactly as I tell you in this letter. Sometime soon I'm going to have to leave you and John, and please stop glaring at this paper, someone is going to think something's wrong._

_First off. Share nothing in this letter with anyone else besides me. Not John, not Mycroft, not a damn person._

_I need you to go to this café- _here he had scribbled the address of a café, the one she was sitting at –_and wait there for me. Be there no later than 8:30. I'll be there as soon as I possibly can. Don't panic if I don't recognize you; I probably won't. Give me the key. If I ask how you got it, show me the envelope. It'll clear up the confusion._

_Should I ask for more information, only if I do, I need you to tell me something, Irene. I told you only once, and I hope that you remember it. But I won't write it here- you'll know exactly what to say when the moment arises._

_Follow these instructions, Irene. I'll see you as soon as I can._

_-SH_

So here she sat, dressed up, waiting for him. Her eyes kept darting towards the door, waiting for him to make an appearance. But still, it'd been nearly twenty minutes, and the clock was ticking.

A gust of bone chilling wind swept in as someone walked through the door, taking in his surroundings quickly. A long black coat, a dark blue scarf… Irene got up swiftly, crossing over to him and throwing her arms around him, squeezing him tightly.

"You came. God, I was going to say, you were almost late! I would've murdered you. No, I really wouldn't have, I was kidding." She tugged him over to the table she'd been sitting at, smiling up at him as she sat down. "What? What's wrong, you look like you've forgotten something important again."

"Forgive me for asking, but who are you?"

_**Hehe. Let me know how I'm doing so far!**_

_**The thought of Irene Adler in Torchwood both enthralls and terrifies me. I'm just saying.**_

_**Next chapter: Irene follows instructions, the TARDIS is sick, and we see a few old friends...**_


	3. Chapter 3

_**I'M SO SORRY GUYS FORGIVE ME PLEASE PLEASE PLEASE. I've been so freaking busy, you don't even understand.**_

_**ALSO. SCANDAL IN BELGRAVIA OMFG OMFG OMFG I JUST CAN'T OKAY. IRENE BAMF ADLER. **_

_**Disclaimer: Not mine. **_

"Excuse me? It's me, it's Irene…" She recalled the letter, her face falling slightly. "Sorry, you look like someone very dear to me."

"Not a problem!" The Doctor grinned at her. "It happens to the best of us."

"Yeah…" What was she to do next? Her mind raced frantically. The key! She dug through her bag and pulled at the tiny silver key, holding it out on her hand to the Doctor. "I'm supposed to give you this. Here." Hopeful eyes followed his movements.

The Doctor took the key from her hand slowly, turning it over and over, his eyes wide in shock. Impossible. Absolutely, positively impossible. "How… how did you get this? Where did you get this from?" He stood up, towering over her. The force of the Oncoming Storm raged in his eyes. "Who gave this to you?"

Irene was taken aback by the anger and terror in his eyes. "Hang on a moment," she muttered, digging through her purse until she came across the envelope. "I'm supposed to show you this." She pulled the letter out and hung onto it, passing the envelope to the Doctor. "Does that help?"

The Doctor took the familiar blue envelope, his hands trembling. "I d-don't understand," his voice cracked. "How could you… But… I don't understand." He stared at Irene in confusion. "Who are you? Tell me!"

Irene stared at him, worry written on her face. _Should I ask for more information, only if I do, I need you to tell me something, Irene. I told you only once, and I hope that you remember it. But I won't write it here- you'll know exactly what to say when the moment arises. _

She was thinking rapidly, her mind racing through the stolen moments they'd shared during cases, when John wasn't looking. She remembered the secrets whispered in the dark of the night, the knowing glances during the day. And she remembered a word- a name he'd told her one night, not long before he'd disappeared, a name he told her would be important, that was meant for her ears only. He'd told her it one night while they were in bed, foreheads pressed together. He said it only once, but she remembered it.

Irene looked up at the Doctor, standing swiftly and putting her hands on his shoulders, pulling herself up a tad so she could whisper the name in his ear, her breath caressing his ear as she did. The silver key slid out of his hand, dropping to the floor with a tinny clink. The look of shock on the Doctor's face was unseen by the brunette, who crouched down to pick it up. "You dropped this." She stood back up, sliding it back into his hand. "Was that worth anything?"

"That was my name." The Doctor's voice was barely above a terrified, strained whisper. His eyes swung down to meet hers, terrified blue-gray locking on warm hazel. "Nobody knows my name, I can only tell somebody my name for one reason…" His voice shook. It was River Song all over again. He couldn't. He wouldn't. Shaking, the Doctor sat down, slipping the key and envelope into one of his pockets.

A frown appeared on Irene's face as she watched him. Before she could stop herself, she had kneeled in front of him, one hand resting on his knee as she looked up at him. Her touch sent a jolt through the Doctor, who jumped slightly, causing Irene to move back a tad. "Are you alright?"

"Yes, yes, perfectly fine." The Doctor's tone suggested anything but fine, and it didn't help that he had his head in his hands. Something clicked in his head. "What was your friend's name?"

"Sherlock. Sherlock Holmes." Irene stood and looked him over for a second. "You do remind me of him. Strange." She picked up her purse, sighing slightly as she nodded at him. "Well. Good night." And with that, she disappeared, leaving the Time Lord to figure out exactly just what happened.

-o-o-o-

"Morning, Irene." Jack looked over the top of his newspaper at her, smirking at her outfit. It was almost as if she really just wanted to torture the male species. Tight black pants, a short black dress, and a long khaki coat put with a pair of heeled boots… he just couldn't help it. "How many men did you kill with your outfit this morning?"

"Shut up." She rolled her eyes. "I see you're still in the same outfit. Don't you ever change?"

"Nope. How did your thing go last night?" Refolding the newspaper and setting it on his desk, Jack leaned forward, curious. Irene sighed, walking off to her own desk and getting on her computer, typing furiously. Giving her a roll of the eyes, Jack pushed himself up and out of his chair, leaning on the back of hers. "Did it really end that badly?"

"It went fine."

"Sounds the opposite." Jack pushed a few files away and sat on the edge of her desk.

"God, Jack, please, shut up."

Footsteps approached the two. "Oh, I hear you two arguing again, what's it about this time?" Gwen Cooper complained slightly, frowning. "Honestly, might as well go turn some of that frustration into something better."

"Nice to see you too, Gwen, but _the Captain_ won't leave me alone!" Irene only ever referred to him as such when she was angry.

"I'm simply enquiring as to the nature of the thing you ditched me for last night."

"Jack, leave her alone!" Gwen gave him a glare that shut him up immediately. "Can't you two stop acting like children for ten minutes?"

-o-o-o-

_Time Vortex_

The Doctor had rushed back to the TARDIS, going back inside and examining the key again. It was a plain TARDIS key; nothing was strange about it at first glance. A small etching near the top caught his attention, and he squinted his eyes at it curiously. _SH_

Could he really have gone back and lived out a… a domestic life with this woman? She seemed nice enough, pretty too.

No. He wouldn't have. She could be another companion, and he swore he'd never take one on again, not after the Ponds and what happened to them.

"I'm not dealing with this again," he muttered, running to the console and flicking switches. The Doctor was running again, he wouldn't go through the heartbreak he'd endured with Rose and River again.

The TARDIS shuddered, the familiar noise of grinding accompanied by a harsh sounding wheeze. The Doctor frowned. "What's wrong, old girl?" he said, rubbing the console, checking the view screens. Nothing was really out of the ordinary here, but yet… "Let's try this." He flicked a lever, pumping another quickly.

The TARDIS lurched violently, sending the Doctor to his knees. Concern was written on his face as the ship shook, the Doctor struggling to his feet. Buttons were pushed, levers were flicked, things were spun, but the TARDIS continued to shake. He gave up, instead clinging onto the console for dear life as the TARDIS plummeted towards Earth.

-o-o-o-

_London, October 2010_

The Doctor coughed, stumbling through the cloud of smoke and pushing the door open, falling out of the TARDIS, wheezing. She had crashed in an alleyway, somewhere in London, he recognized the surroundings. He didn't know the exact date, and quite frankly he didn't want to know. He wanted to get away from Earth, as quickly as he possibly could.

Poking his head back inside the TARDIS, he pulled the sonic from inside his coat, trotting to the console and scanning it. It emitted a series of loud beeps, frowns creasing the Doctor's forehead. "Oh, that's bad. That's very bad." He tried to move a few levers, but they were all stuck. "Come on, old girl!"

Several hours later, the Doctor had to accept the inevitable. The TARDIS wasn't going anywhere. He was stranded. He, the Doctor, the Oncoming Storm, stranded in the middle of London with a sick TARDIS and absolutely no way of making a life for himself here.

"This is bloody wonderful."

_**Poor bby~**_

_**Let me know how I'm doing!**_

**_Review? Please?_**

**_Next chapter: Mycroft appears, the Doctor takes on a new name, and the first case..._**


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